To meet the growing railway-transportation demand, researchers have designed a new train control system, communication-based train control (CBTC) system, to maximize the ability of train lines by reducing the headway of each train. However, wireless communications expose the CBTC system to new security threats. Due to the cyber-physical nature of the CBTC system, a jamming attack can damage the physical part of the train system by disrupting the communications. To address this issue, this chapter develops a secure framework to mitigate the impact of the jamming attack based on a security criterion. At the cyber layer, we apply a multi-channel model to enhance the reliability of the communications and develop a zero-sum stochastic game to capture the interactions between the transmitter and jammer. We present analytical results and use dynamic programming to find the equilibrium of the stochastic game. We investigate a special case study to obtain insight results, showing a strong inter-dependency between the physical and cyber layers. Finally, the experimental results are provided to evaluate the performance of the proposed secure mechanism.